Chapter 18- Unit 4

Question 1

what is alternative splicing?

Answer 1

it is the ability to produce different proteins from the same mRNA by splicing together different combinations of exons

Question 2

what kind kind of example is calcitonin/calcitonin gene-related peptide gene (CT/CGRP)

Answer 2

alternative splicing

Question 3

what is the function of calcitonin in the thyroid gland

Answer 3

it reduces blood calcium levels

Question 4

what is the function of calcitonin gene-related peptide gene (CT/CGRP) in neurons?

Answer 4

it dilates blood vessels

Question 5

how many poly A tails are there in the primary transcript

Answer 5

there are 2 tails; 1st one b/w 4 and 5; 2nd one after 6

Question 6

what is myotonic dystrophy (DM)

Answer 6

it is an autosomal Dominican condition characterized by myotonia, insulin resistance, cataracts, intellectual disability, and cardiac muscle problems

Question 7

what kind of example is myotonic dystrophy (DM)

Answer 7

alternative splicing

Question 8

what is DM1

Answer 8

• a type of myotonic dystrophy

- the DMPK gene >150 copies of a CTG repeat (aka a tri-nucleotide repeat expansion disease)

Question 9

what is DM2

Answer 9

• a type of myotonic dystrophy

- the CNBP gene has >11,000 copies of a CCTG repeat ( a tetra-nucleotide repeat)

Question 10

what is DM caused by

Answer 10

it is caused by the build-up of the RNAs in the nucleus, which interfere with alternative splicing regulators important in muscle and neuron function

Question 11

In eukaryotic mRNA what happens if the 5’ cap or the 3’ poly-A tail are lost?

Answer 11

it would result in degradation

Question 12

what are the two mechs of mRNA decay

Answer 12

1. deadenylation -dependent decay

2. deadenylation-independent decay

Question 13

what does deadenylation-dependent decay do?

Answer 13

degrading euk mRNA by removing 5’ cap and 3’ poly-A tail

1. deadenylase shortens poly-A tail
2. exoribonuclease shortens poly-A tail in 3’ to 5’ direction
   3decapping enzyme takes off the 5’ cap
3. exoribonuclease (XRN1) degrades in the 5’ to 3’ direction

Question 14

what does deadenylation independent decay do?

Answer 14

degrading euk mRNA by just taking off the 5’ cap

1. decapping enzyme takes odd 5’ cap
2. exoribonuclease (XRN1) degrades in the 5’ to 3’ direction
3. endoribonuclease cuts mRNA into bits (interanlly)
4. exoribonuclease starts to break up the unprotected fragments that are made from step 3

Question 15

what is nonsense mediated decay?

Answer 15

a cellular response in which mRNA is degraded if it contains a premature termination codon (PTC)

1. Exon junction complex ( EJC; in b/w exons; leave after translation) proteins promote the recruitment of Upf
2. Upfs activate de-capping enzyme (removes 5’ cap)
3. exonuclease/endonuclease degrade mRNA (make mRNA vulnerable)

Question 16

what are small ncRNA (sncRNA; snickers)

Answer 16

the are double stranded RNA molecules with short 3’ overhangs (20-31 nt long)

Question 17

what are the two types of sncRNAs?

Answer 17

1. microRNAs (miRNAs; endogenous)

2. small interfering RNAs (siRNAs; exogenous)

Question 18

wha are micro RNAs (miRNAs) and what do they do?

Answer 18

they are a type of RNA that is encoded in the genome and they regulate the expression of other genes

Question 19

what is RNA interference

Answer 19

it is a mech where sncRNA molecules tell the post-transcriptional silencing of mRNAs in a sequence-specific manner meaning they become slightly complementary to the messenger RNA (mRNA)

Question 20

what do both miRNA and siRNA result in after RNA interference

Answer 20

results in a gene knockdown= knocking down the expression of a gene
by……

1. triggering mRNA degradation
2. inhibiting mRNA translation

Question 21

what is the pathway for miRNA in rna interference

Answer 21

1. miRNA genes are expressed to make primary miRNA (nucleus)
2. drosha enzyme cuts primary mmiRNA to make pre-curose miRNA (and then enters cytoplasm) (nucleus)
3. dicer cuts the pre-curseor miRNA to shorten miRNA
4. RISC (rna induced silencing complex) binds to double stranded miRNA
   
   • AGO (silncer) removes 1 strand, and keeps the other
     
     1. strand=partially complementary= translation is inhibited
     2. strand= totally complementary= mRNA is degraded by RISC

Question 22

what is the pathway for siRNA in RNA interference

Answer 22

1. dicer cuts the pre-curseor siRNA to shorten siRNA
2. RISC (rna induced silencing complex) binds to double stranded siRNA
   
   • AGO (silncer) removes 1 strand, and keeps the other
     
     1. strand=partially complementary= translation is inhibited
     2. strand= totally complementary= mRNA is degraded by RISC

Question 23

what are long ncRNAs (lncRNAs; long nickers)

Answer 23

they are double stranded RNA molcuces (> 200 nt long)

Question 24

what is a function of lncRNAs

Answer 24

they function as competing endogenous RNAs (ceRNAs) and it is where they act as “sponges” and “soak up” miRNAs

Question 25

what is an example of a lncRNA functions as a ceRNA

Answer 25

duchenne muscular dystrohpy - linc-MD1 is low which allows for miR-133 and miR-135 to bind and to prevent the translation of these RTF - could add more linc-MD1 to cure this (maybe)

Question 26

what is an example of lncRNAs

Answer 26

the X inactivation by the lncRNA Xist | - causes the entire chromosome to be inactivated

Question 27

who were the people who showed one of the first examples of RNAi

Answer 27

Andrew Fire and Craig Mello

Question 28

what does mex-3 RNA do in c.elegan embryos

Answer 28

this RNA is expressed formally and when it does this it plays a role in development

Question 29

what is mex-3 antisense

Answer 29

it is the strand that is complementary to sense mex-3 mRNA

Question 30

what were the conditions of the cells in the RNAi experiment

Answer 30

have 4 cells 1. normal 2. endogenous mex-3 RNA 3. injected with mex-3 antisense RNA 4. injected with sense and antisense dsRNA

Question 31

what was the result from the RNAi exxperiment

Answer 31

- when the cell is injected with antisense it losses expression for mex-3 RNA but not completely - when the cell is injected with sense and antisense dsRNA there is no expression of the mex-3 RNA

Question 32

once the cells are injected with stuff in the RNAi experiment what happens next

Answer 32

1. the embryos are put into in situ hybridization 2. a labeled probe is added that is complementary to mex-3 RNA 3. if the cell expresses mex-3 RNA that mRNA in the cells will bind to the probe and become labeled

Question 33

how can the Xist cause the entire X chromosome to become inactivated

Answer 33

Xist can cover many regions on the X chromosome

Question 34

once the X chromosome is inactivated what happens to it

Answer 34

The X chromosome is coated by a stable Xist and it silences and condenses the X chromosome making it into a Barr body